Erratum in

PLoS One. 2014;9(5):e97393.

Abstract

River water is a small percentage of the total freshwater on Earth but represents an essential resource for mankind. Microbes in rivers perform essential ecosystem roles including the mineralization of significant quantities of organic matter originating from terrestrial habitats. The Amazon river in particular is famous for its size and importance in the mobilization of both water and carbon out of its enormous basin. Here we present the first metagenomic study on the microbiota of this river. It presents many features in common with the other freshwater metagenome available (Lake Gatun in Panama) and much less similarity with marine samples. Among the microbial taxa found, the cosmopolitan freshwater acI lineage of the actinobacteria was clearly dominant. Group I Crenarchaea and the freshwater sister group of the marine SAR11 clade, LD12, were found alongside more exclusive and well known freshwater taxa such as Polynucleobacter. A metabolism-centric analysis revealed a disproportionate representation of pathways involved in heterotrophic carbon processing, as compared to those found in marine samples. In particular, these river microbes appear to be specialized in taking up and mineralizing allochthonous carbon derived from plant material.

The GC% profile of the Amazon reads is shown (red) in comparison to a freshwater datasets (Lake Gatun), an estuary (Chesapeake Bay), a typical marine sample (Mediterranean Deep Chlorophyll Maximum) and a soil metagenome (Waseca County Soil).

The tree shows the relatedness of diverse metagenomic datasets based on Jaccard distance derived from all versus all comparisons of reads with BLASTN. Datasets of different salinities were chosen for the comparison. Freshwater: Amazon, Lake Gatun; Marine: Mediterranean DCM, Sargasso Sea GS000a, HOTS 4000 m; Hypersaline: Punta Cormoran 6% (salinity) and Santa Pola salterns of three different salinities 19%, 32% and 37%). Waseca county soil dataset was used as an outgroup to construct the tree (see ).

Phylogenetic profile of the Amazon metagenome is shown using two different approaches, one, using the 16 s rRNA sequences gathered from the metagenome, and the other using all the reads and comparing against sequenced microbial genomes (using the MG-RAST server).

The GC% of all reads assigned to actinobacteria in different datasets is shown. Datasets shown are the Amazon metagenome (red), Lake Gatun (black), HOTS 4000 m (deep blue), Waseca County Soil (Brown). The inset shows the % of actinobacterial reads in each dataset.